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For a list of markers, see Category:Immunohistochemical markers.

While microsopic examination using standards stains may be sufficient for diagnosis, the use of immunohistochemistry to identify specific antigens can be used to confirm diagnosis or to narrow down when there is doubt (e.g. poorly differentiated carcinomas where the origin may allow more tailored chemotherapy). The expression of certain antigens can be pathognomonic of certain diseases or pathologies.

Like all tests, immunohistochemistry is subject to the same limits of imperfect sensitivity and specificity. Traditionalists decry the over-reliance on expensive immunohistochemical stains which can often behave capriciously and are sometimes used indiscriminately when careful study of the morphological features on standard haematoxylin and eosin staining would suffice for diagnosis. At the opposite end of the spectrum, immunohistochemistry has allowed characterisation of tumours that in the past would have been described simply as undifferentiated tumours or erroneously classified as another tumour type. One should strive for a happy medium.

The nomenclature of immunohistochemistry can be confusing as positivity may be described both in terms of the antigen as well as the antibody. This is largely a historical legacy of a time when our ability to make antibodies outstripped our ability to identify either the corresponding antigen or its function. An example of this is the clusters of differentiation where antibodies were available long before the functions of the antigens were elucidated.

In the case of Ki-67, Ki-67 may refer to both the antibody or the antigen.

Another reason for the confusion is that certain antibodies may recognise epitopes that may be present in more than one protein, e.g. CAM 5.2 is thought to recognise more than one cytokeratin.